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ltr-retriever 2.9.4 (#38300)

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snehring 2023-06-12 03:05:44 -05:00 committed by GitHub
parent 41345d18f9
commit 4cc5e9cac6
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GPG Key ID: 4AEE18F83AFDEB23
2 changed files with 38 additions and 1 deletions
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10
var/spack/repos/builtin/packages/ltr-retriever/package.py
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@ -15,6 +15,9 @@ class LtrRetriever(Package):
homepage = "https://github.com/oushujun/LTR_retriever"
url = "https://github.com/oushujun/LTR_retriever/archive/v2.8.7.tar.gz"
maintainers("snehring")
version("2.9.4", sha256="a9f4668113d2d75ab97cd85b456f11b00afd4876848a8ef099622ec0d9e505e7")
version("2.8.7", sha256="29ca6f699c57b5e964aa0ee6c7d3e1e4cd5362dadd789e5f0e8c82fe0bb29369")
depends_on("perl", type="run")
@ -22,6 +25,7 @@ class LtrRetriever(Package):
depends_on("hmmer@3.1b2:", type="run")
depends_on("cdhit", type="run")
depends_on("repeatmasker", type="run")
depends_on("py-tesorter", type="run", when="@2.9.4:")
def install(self, spec, prefix):
filter_file(r"BLAST\+=.*", "BLAST+=%s" % spec["blast-plus"].prefix.bin, "paths")
@ -29,8 +33,12 @@ def install(self, spec, prefix):
"RepeatMasker=.*", "RepeatMasker=%s" % spec["repeatmasker"].prefix.bin, "paths"
)
filter_file("HMMER=.*", "HMMER=%s" % spec["hmmer"].prefix.bin, "paths")
filter_file("CDHIT=.*", "CDHIT=%s" % spec["cdhit"].prefix, "paths")
filter_file("CDHIT=.*", "CDHIT=%s" % spec["cdhit"].prefix.bin, "paths")
filter_file("BLAST=.*", "", "paths")
if spec.satisfies("@2.9.4:"):
filter_file(
"^TEsorter=.*$", "TEsorter={}".format(spec["py-tesorter"].prefix.bin), "paths"
)
mkdirp(prefix.opt)
mkdirp(prefix.bin)

29
var/spack/repos/builtin/packages/py-tesorter/package.py Normal file
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@ -0,0 +1,29 @@
# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class PyTesorter(PythonPackage):
"""
TEsorter is coded for LTR_retriever to classify long terminal repeat
retrotransposons (LTR-RTs) at first. It can also be used to
classify any other transposable elements (TEs), including
Class I and Class II elements which are covered by the
REXdb database.
"""
homepage = "https://github.com/zhangrengang/TEsorter"
url = "https://github.com/zhangrengang/TEsorter/archive/refs/tags/v1.4.6.tar.gz"
maintainers("snehring")
version("1.4.6", sha256="c6952c98fa78d0084742fd6c7d2d1204d36db103c3cbeb19e52093cd9d311523")
depends_on("py-biopython", type=("build", "run"))
depends_on("py-xopen", type=("build", "run"))
depends_on("hmmer@3.3:", type="run")
depends_on("blast-plus", type="run")